When the Pup Grows Up
by ashowofhands7
Summary: An alternate story line beginning at the start of season 3, Beckett and Castle are thrown back together in the aftermath of a terribly tragedy. The discovery of a new, insane, cruel, and brilliant villain will test their relationship, resolve, and make them question their very actions.
1. Chapter 1

This story takes place at the beginning of season 3. Everything up to that point remains the same. Kate broke up with Demming in order to express her feeling for Castle but before she does, she is interrupted by his ex-wife Gina. It is then revealed that they have started a relationship together again. They then part for the summer.

* * *

"In individuals, insanity is rare; but in groups, parties, nations and epochs, it is the rule." – Friedrich Nietzsche

-Sometime in early July-

A mysterious figure appears in front of a large group of people. The room in which they are all located in very dark and dusty. It is an abandoned building in the Bronx. The crowd is deathly silent as the mysterious figure centers himself in front of them. His cold presence falls over the room causing goosebumps to appear on many of his guests.

"My… my… my…" He begins to walk around his home made stage. His shoes cause loud footsteps in the quiet room, sending chills up the spines of his crowd. "It saddens me to see so many of you here today." he pauses. "For whatever reason, you are all here because you have been hurt. Hurt by the very city in which you live."

Many of the guests begin to shift their eyes from one another, from the accountant to the teacher.

"Those who claim to have your best interests at heart have come and they have taken your families…., ruined your careers…., corrupted your friends against you…., crushed your very hopes and dreams…."

Many of the crowd began feel more at ease. Some shed a tear while other clenched their fists.

"I say, no longer. I say, we show these people that they cannot treat us this way. I say, that we show them that there is a price to be paid for the lives they have destroyed!" His voice grew louder and more ferocious.

The crowd began to get a little louder as members began to shout things like "Damn right!" or "Make them pay", a couple members clapped a couple times before he continued.

"You've all been following my letters. You've listened to my teachings. You have cheered and cried and now you will come together as a community…. We will have our revenge. We will turn this city against itself. We will show the people of New York City that when an abused puppy grows up, it bears the teeth and the hate that allows it to tear apart is abuser."

The crowd was on its' feet now. Some were cheering others stood in complete admiration the mysterious figure. One thing is for sure. There wasn't a single person in that abandoned building that disagreed with him. They knew his promises rang true.

"In two months' time, we will set our plan into action, and we will have our revenge!"

* * *

-September 2nd - 12th Precinct—

Kate Beckett stared at her phone just waiting for it to ring. When Castle had left in May, he said that he would return in the Fall. They knew that he had come back four days ago, but no one had heard from him. After the way that she had left things with him, her summer took a turn for the worse. The first month, she was train wreck. She envisioned Castle with Gina and it tore her apart. She was eventually able to move on. She had been on dates that turned into short relationships that were mostly physical. None of them lasted.

Esposito and Ryan were up to some shenanigans in the office again. It was a sight that made her giggle as Ryan had accidentally dropped an egg off his desk and it had landed on Esposito's Italian shoes (which he wore to the office in order to show off). Esposito chased after Ryan between desks, through rooms, and behind the investigation board. Kate had missed their goofing off. It wasn't as common an occurrence as it was when Castle was around.

After Esposito caught and punished Ryan to the appropriate extent he came over to Beckett's desk.

"Hey, I'm sure he'll call. You know Castle, he never does things exactly how you expect he would" Esposito said in a reassuring tone.

"That's just it Esposito." Beckett replied. "I do know Castle and you were right. There wasn't a reason for him to stay anymore."

"Kate…"

"Look, I don't want to talk about this, especially at work. Can we just focus on our latest case?"

"Yeah. Sure." Esposito paused for a second and then picked up a case file. "Caucasian. Female. Age 26. She was found with her neck crushed by a window. No prints on the window but we did find some interesting substances in her apartment."

"Alright, let's head down to the crime scene to investigate and have Ryan look up the usual suspects. A boyfriend, coworker, and let's see if we can find a drug connection here."

"Sounds good" Esposito ran over to his desk and grabbed his coat. He tapped Ryan on the shoulder and told him what Beckett had said.

Beckett pulled her gun out of her desk and holstered it. She grabbed her light leather jacket and strapped her badge onto her belt before grabbing the car keys. Suddenly, there was an enormous blasting sound coming from outside and the 12th Precinct shook throwing Beckett, Esposito, and Ryan to the floor.

* * *

-September 2nd – Richard Castle's Apartment-

Alexis and her father struck their replica lightsabers together and attempted to get an upper hand in the struggle.

"I sense great fear and hatred in you" Castle said in a goofy high pitched voice. "Search your feelings you know it to be true"

Alexis broke away from the struggle and jumped off of a chair to deal a high strike to her father's arm. In the spirit of the game they were playing he fell to the floor and his lightsaber rolled slightly away from him. Alexis held her lightsaber at Castle's throat as he froze for this would surely be his demise.

" You cannot defeat me," Alexis said dramatically. "for there is something that you do not know."

"I know it all!" Castle responded in a goofy, yet dramatic fashion. "You kidnapped my long lost daughter!"

"No… I am your daughter!"

"That's not true that's IMPOSSIBLE!"

Suddenly Martha walked down their stairs. "Will you two grow up already?"

Castle jumped up to meet her in the kitchen. "I'd like to see you make me."

"What are you? Five?"

Castle giggled "Try twenty-five"

"Try forty-two" Alexis chimed in. "Dad, are you sure you aren't going to call into the precinct? You really seemed to enjoy it there and after spending most of the summer alone in the Hamptons, it could be good for you to go back"

"Now Alexis" Castle said matter-of-factly, "Just because Gina left after the first couple of weeks doesn't mean I didn't have a good time. In fact, I think you are confusing my state of mind with how it would be if she had stayed."

Alexis laughed. "Seriously Dad…"

Castle sighed. "I just think that period of my life is done, pumpkin. I may call to see if I can catch up with some of them over a beer but I don't see myself going back."

"But…"

"No buts!" Castle turned his daughter toward the stairs. "Now go get your things ready for school."

Alexis ran up the stairs a little bit pouty but Castle knew she wasn't really serious about it. He walked over to his office and sat down at his desk. He flipped open his laptop to see if there was any news about his upcoming book "Naked Heat." He felt himself feeling a new kind of stress unknown to him before as he continued to write about the character he based on Beckett. He just had to accept the fact that he was moving on. There was nothing in his email about the book so he closed his laptop and picked up his coffee mug. He sighed as he looked into his expresso and remembered when he brought in the expresso machine for the Precinct. He was going to miss it. He stared out of his window, out to see the New York skyline when it happened. He dropped his expresso and the cup shattered into several pieces at his feet. The coffee went everywhere and began to burn his feet. He didn't notice at first but he wasn't standing there very long.

A loud blast sound happened and then shook the building slightly. He slipped as he ran to the kitchen. Alexis ran down the stairs clumsily screaming in terror.

"Alexis!" Castle shouted "Alexis! Are you alright?"

Alexis finally got to the bottom of the stairs and ran into her father's arms.

"What's happening Dad?" Alexis shouted as she began to hyperventilate.

Castle held his daughter close and her breathing began to slow down. His heartbeat, however, was beating extremely fast and it wasn't going down. It wouldn't slow down for a very long time after what he had seen…. He had just seen the top of the Chrysler building explode…

* * *

Hey. If you are reading this then thank you! I would love to hear what you think of the story thus far. I'm planning on diving more into the vulnerabilities of each of the characters. I'm also planning on going into a more linear storyline rather than a case by case type of deal.

If you would like to favorite or follow, I would greatly appreciate it and please drop me a review!


	2. Addressing the Nation

"It is by presence of mind in untried emergencies that the native metal of man is tested." –James Russell Lowell

* * *

-September 2nd –

The explosion in the building originated was centered at the top of the building. The spire began to tip over. The cringe-worthy sounds of ripping metal filled the city. The top of the spire struck a nearby building on its way down, throwing metal and concrete flying into the street below. People below ran for their lives and the spire continued its' path downwards but not everyone was lucky enough to get away. Cars were crushed as pieces of the building broke off and fell without resistance. Finally the spire reached the street and an incredibly loud crushing sound echoed through the streets of New York. A shockwave threw people to the ground as the impact struck. The destruction of the street was devastating. It was not the first time, and it wouldn't be the last but on that day New York City stood still.

-Richard Castle's Apartment-

"Dad, what are you thinking?" Alexis pleaded with her father. "You can't go out there. It's way too dangerous"

Castle threw on a jacket. "We are only five blocks from the Chrysler building. The streets are jammed right now. I can run over there and see what I can do." Castle was already breathing hard. His adrenaline had kicked in and things seemed to be moving slower to him.

"Are you insane?" Martha sided with Alexis. "I know you've always been a little nuts but this is suicidal!"

"Look, I just have to go." Castle opened the door to leave. "I can't just stay here when I know I could help someone. Lock the door behind me and don't let anyone in."

Castle left and ran down the stairs. For some reason, he didn't trust the elevator. It was a very long way down but with his body pumping adrenaline into his system, he didn't seem to feel very tired. He reached the street and bolted out the door to see an enormous traffic jam. Many people were running, some toward the incident to either get a closer look or help, others ran away from the wreckage. Many people had abandoned their cars and this was the main reason for the traffic jam. Castle joined those running toward the building. As he turned the final corner he was finally starting to feel the effects of running so much. The adrenaline was wearing off but he knew he couldn't slow down now.

Despite living in New York for most of his life, Castle was not in the city at the time of the September 11th terrorist attacks. Despite that event, he didn't think anyone could have gotten used to the site he saw before him. He looked at the enormous amount of destruction and didn't know if anything could have prepared him for it. There were enormous slabs of concrete everywhere. There were cars that had been crushed by the falling debris that were bent into shapes he hadn't even seen at a car dump (which he visited while writing one of his Storm books). A constant flow of people were trying to escape the scene and the crowd exiting the remaining part of the Chrysler building seemed to be overflowing the doors.

Castle began to move forward towards the wreckage. He saw some victims that had been unlucky and hit by pieces of falling debris. People called out to him to help but most of them were under tremendous sections of concrete. He wouldn't be able to help them. They would need a serious equipment to free those people if they hadn't bled out by then. Sirens were blaring in his ears causing them to ring. Enter so foolhardily had caused him to become a bit disoriented.

Then he saw a group of people working together in order to life a large (but manageable) piece of concrete that had crushed the legs of a man. Castle rushed over and was able to get a good hold on the slab. As more people joined in, it began to lift slowly. Eventually they were able to life enough that someone could pull the man out from under it.

"Okay everyone! Watch your hands and feet and let it drop!" Castle recognized the voice and after everyone had put the concrete down safely he turned and recognized someone run over to the victim.

"Esposito?" Castle was shocked to see him. He knew that the Precinct was close but his apartment was much closer. How could he have gotten there first?

"Castle?" Esposito looked even more shocked than Castle.

"How did you get here so fast?"

Esposito looked confused. "What do you mean? We were on the scene twenty minutes after the explosion."

Apparently with him getting ready, taking the stairs, running five blocks, and walking through the wreckage disoriented, he had taken more time than he originally thought. Esposito must have gotten in a vehicle almost immediately.

"Castle, what are you doing here?" Esposito interrupted Castle's thoughts. "You need to get home and stay with your family."

"Come on Esposito!" Castle argued. "I'm here to help. Considering the large traffic jams throughout the city right now, I'm assuming that you are low on manpower." Esposito didn't make an effort to argue his point. "You know me. I can help. At least until the police force is here in bulk."

Esposito was quite for a second but decided he had to think fast. "Alright Castle, but you have to do exactly what I tell you. "

"You got it."

"Alright the priority is to get people out of the area. It seems that the tower is holding steady but for all we know it could collapse at any minute. We need to direct the crowd in a safe distance so people are running randomly in a panic."

* * *

-12th Precinct-

Kate awoke and realized a pain on the top of her head. When the precinct shook, she had been throw to the floor. As she slid on the smooth floor she had bumped her head fairly hard and it had knocked her out. She had awoken to Lanie checking her vitals. She heard the Chief's voice echoing in the room as he shouted orders.

"Kate… Kate!... KATE!" Lanie was trying desperately to get Beckett's attention.

She finally snapped out of it. "What?" Kate asked quietly, still a bit disoriented.

"You suffered a slight head injury that knocked you out. How do you feel?"

Beckett finally came back fully. "What was that shaking?... and that sound?"

"Don't worry about it. Now tell me how you feel! I need to know if you got a concussion."

"I'm fine!" Beckett said a bit too firmly. "Now tell me what's happening!"

Lanie sighed. She knew Beckett wouldn't let up on this. "It seems that there was an explosion at the Chrysler building."

Beckett realized it then for the first time that despite her calm manner, Lanie was shaking. "How bad?"

"The spire of the building crashed down on the street below…"

Beckett grabbed Lanie by her shoulders and held her grip tightly. "Do what you have to do to make sure I'm okay and do it fast. I need to get out there."

* * *

Esposito and Castle had been able to successfully steer the crowds of people in the right direction until back up arrived. Without having proper gear Castle and Esposito were told to go back to the temporary control base that they had set up a couple blocks away. When there they were checked for injuries and despite Esposito's objections, neither of them were allowed to return to the wreckage as the police force was at full strength and had the situation under control. Beckett had been cleared by Lanie and soon met up with Ryan at the wreckage. They both assisted the fire department in freeing most of the citizens trapped under rubble. Those badly injured were either treated at a nearby medical station that was set up, or transported to a hospital if it was bad enough. The rest of the Chrysler building was able to remain standing. Much of the inside was badly damaged by the blast and the shock it caused but the main supports were still intact which kept the building standing. Everyone was able to keep busy and help but at midnight, the President had scheduled an address to the public. The world would stand still during this moment and few would forget what happened.

* * *

-September 3rd, Midnight-

All eyes were glued to the television as the Presidential Seal appeared on the screens with the words "Please stand by" underneath it. Soon the seal faded and there sat the President of the United States, sitting in the oval office.

"My fellow Americans, today we have suffered a great tragedy. At exactly 7:50 A.M. an explosion occurred near the top of the Chrysler building in New York City. The explosion separated the top of the building from the rest and the momentum created by the blast forced the spire to plummet to the street below. As of right now we are working with the military and choice experts to determine what happened…. At this time, it would appear that the explosion was not an accident… Today wasn't just a tragedy, it was an attack…" The President continued on for a while before leaning forward onto his elbows. "Citizens… I promise that whoever has done this will be brought to justice. There is a price to be paid for attacking this great nation and I will not back down until I find whoever is responsible. I must leave you now. My fellow citizens… Good—"

The feed was suddenly cut off and static was what remained. It remained there for a minute when suddenly the picture returned. However, this time it was not the President and it was not the Oval Office. Instead there appeared a white wall with dim lighting and a masked figure sat there instead. The mask was made of metal and loosely resembled a human face. However, the face was far too skinny and it seemed to give the impression of the human skull as opposed to a face. The figure wore a black hood over his head and had something dark covering his skin. Nothing about his appearance indicated who he was.

The masked figure clapped for a second and gave a sinister laugh. "Well said Mr. President. Bravo indeed." He stopped clapping and leaned forward, placing his hands on his knees. "Well, I have something to say as well, so I hope you will forgive my interruption." He cleared his throat. "Citizens of America, today was a historic day in your history. Today will be the day that I first appeared to you. Today, I destroyed the Chrysler building." He paused for a second. "You see, Mr. President, while you sit up there on Capitol Hill in your cozy office on Pennsylvania Avenue, there is a world that you have turned a blind eye to. Citizens of your country are dying and suffering at the hands of others. They are victims of corruption, disease, and cruelty. I am here to speak on behalf of these people. The city of New York has abandoned us. The city has beaten us, robbed us, brutalized us and now they want to pretend we don't exist. But yet…. you do nothing. Well Mr. President, I say no more. So today, I struck back at the city that hates us… and it is only the beginning. I will turn this city on its' head and soon the entire city will be infected with my hatred… OUR HATRED!... I am something of a fortune teller, Mr. President. And I see chaos in your future… and it is glorious! You will be hearing from me soon. So sorry to interrupt you…"

The feed cut out and was quickly changed to local news programs but nothing was said as the New York City, The United States of America, and the world sat in silence.

* * *

Hope you guys like this chapter. I know that it seems like there was a lot of big speeches and I promise it won't be like that all of the time. But I felt that it was appropriate for this part of the story. Would love to hear feedback. Thanks for reading!


	3. Embarrassing Blunder

"The past is never dead. It's not even past." – William Faulkner

* * *

-12th Precinct-

Beckett and Ryan arrived after being called back by Montgomery. As they walked in they noticed a well-dressed man conversing with the Captain.

"Captain," Beckett began. "why did you call us back? There is still a lot of work to do."

"Detectives," Montgomery looked angry. "this is Agent Fallon with the Department of Homeland Security. He's heading up the investigation to find the terrorist."

"Nice to meet you, Detectives." Fallon walked over to the white board which he had already taken over and set up. "Homeland Security is being spread out to all major cities in case there is a second attack. I don't think that there will be but it's protocol. We are enlisting the help of local agencies and police forces to deal with this crisis now that we are so spread out."

Montgomery turned to Beckett. "I told him that he could expect our full cooperation."

"Alright. What's the current situation?" Beckett was jumping at the chance to take down the one responsible for this.

"Well, as I'm sure that you saw, the terrorist addressed the world 15 minutes ago." Fallon began. "It turns out that he was somehow able to infiltrate the major networks with a dormant computer virus. The virus didn't affect anything until he took over the screens around the world. Then it activated and prevented the shutting down of any feeds. That's why he was able to stay on screen without being cut off."

"Well, he had to be transmitting a signal from somewhere. Can't we track that signal back to its location?" Beckett asked?

"Yes. In just under a minute the trace will be complete and we will receive a location. I've got a SWAT team already prepped. I plan on going with them. You are welcome to join us."

"Wouldn't miss it."

At that second, Fallon received a text.

"Alright people, we got a location in the Bronx. I'm uploading it to your GPS system." Fallon hit a few buttons and soon everyone had a location. "Let's go get this son of a bitch."

* * *

-Abandoned Warehouse in the Bronx-

SWAT had set up by the time that Beckett, Ryan, and Fallon arrived. They quickly fell into position and the Fallon ordered the breach. The agents broke down the door and quickly swept the building. As they entered near the rear, Beckett was able to hear the voices saying "CLEAR!" all around. They slowly moved up floor by floor. When they reached the third floor they found the equipment used to record the video along with the set. It was here that the video was recorded. After SWAT had cleared all eight floors, it was clear that the terrorist had already fled.

"Damn it!" Fallon yelled and then pulled out his cell phone. "The terrorist fled the scene. I want any traffic or security camera footage that could tell me where he went. If he fled in a car, get me the license plate number."

Beckett and Ryan began to search the third floor set to find any sort of clues. The CSU would soon be here to dust for prints and try to find any tiny clues that could give them an edge. Ryan was looking at the video camera that was used when he found a letter that had the letters NYPD written on the front of the envelope.

"Beckett! Fallon!" Ryan yelled out. "I found something."

Beckett and Fallon rushed over to him and Ryan gave the note to Fallon.

"I think it was left by the terrorist for us." Ryan deduced.

Fallon opened the envelope in a rushed and frustrated manner. Then as he pulled out the note, a large amount of white powder fell out. Fallon's eyes grew wide with fear and he pulled out his radio.

"Anthrax! Anthrax!" Fallon yelled into his radio. "Quarantine this area immediately! Nobody goes in or out."

* * *

-Two Hours Later-

The area had been quarantined and several hours later a scientist walked into the building, no longer wearing as hazmat suit. She walked up to Agent Fallon and gave him the news.

Fallon pulled out his radio. "False alarm, there is no contamination. You are free to leave the area." He put his radio away and walked up to Ryan and Beckett. "It's powdered sugar. Seems our terrorist thought he would play a practical joke on us." He paused. "Look we lost a couple hours because I didn't follow protocol. I made a mistake but we have to play catch up now. I doubt that there is anything in the letter that is useful but read it just in case, then meet me back at the station."

Fallon handed Ryan the letter and then walked off. Ryan and Beckett looked at the letter that was still dropping powdered sugar onto the ground.

The Letter was short and read, "Dear NYPD, your organization has been at the center of many cruelties caused by this city. If you could hear the sheer number of stories I've heard about your wrong doings, it would bring you to tears. I even have my own story of your disregard for the citizens of this city but that's not important. I just wanted you to know that I will be coming for you, and I hope you enjoyed my little present. I'm sure you were horribly inconvenienced. P.S. Say hello to Detective Beckett for me and tell her I will be seeing her soon."

"Beckett?" Ryan seemed confused. "This guy seems to know you personally."

"How is that possible?" Beckett asked.

"Well could it have been someone you arrested before? Could any of your arrests have the ability to pull something like this off?"

"How should I know?"

"Come on Beckett! This guy obviously knows who you are! Think!"

"I don't know!"

* * *

Hope you guys liked this chapter . Leave a review if you want. I am always glad to have feedback. Hopefully, I'll be able to update soon.


End file.
